Merge pull request #49 from ekluzek/slim_in_dev_cime

Starting point of SLIM in the cesm2_3 development version of CESM

.config_files.xml

@@ -17,10 +17,13 @@
     <type>char</type>
     <default_value>unset</default_value>
     <values>
-      <value component="slim"      >$SRCROOT</value>
-      <value component="dlnd"      >$CIMEROOT/src/components/data_comps/dlnd</value>
-      <value component="slnd"      >$CIMEROOT/src/components/stub_comps/slnd</value>
-      <value component="xlnd"      >$CIMEROOT/src/components/xcpl_comps/xlnd</value>
+      <value component="slim"                       >$SRCROOT</value>
+      <value component="dlnd" comp_interface="mct"  >$SRCROOT/components/cpl7/components/data_comps_mct/dlnd</value>
+      <value component="dlnd" comp_interface="nuopc">$SRCROOT/components/cdeps/dlnd</value>
+      <value component="slnd" comp_interface="mct"  >$SRCROOT/components/cpl7/components/stub_comps_mct/slnd</value>
+      <value component="xlnd" comp_interface="mct"  >$SRCROOT/components/cpl7/components/xcpl_comps_mct/xlnd</value>
+      <value component="slnd" comp_interface="nuopc">$CIMEROOT/src/components/stub_comps_nuopc/slnd</value>
+      <value component="xlnd" comp_interface="nuopc">$CIMEROOT/src/components/xcpl_comps_nuopc/xlnd</value>
     </values>
     <group>case_comps</group>
     <file>env_case.xml</file>

.gitignore

@@ -3,6 +3,9 @@
 manage_externals.log
 cime/
 components/
+ccs_config/
+libraries/
+share/
 
 # ignore svn directories
 **/.svn/**

CONTRIBUTING.md

@@ -4,17 +4,17 @@ We recommend that you first open an issue (https://github.com/escomp/ctsm/issues
 discuss the changes or additions that you propose. You should also contact some of the responsible 
 individuals for SLIM and run by the changes with them.
 
-Erik Kluzek -- Software Engineering ([email protected])
-Marysa Legue -- Originator ([email protected])
-Isla Simpson -- Principal Investigator ([email protected])
+Erik Kluzek -- Software Engineering ([email protected])  
+Marysa Lague -- Originator ([email protected])  
+Isla Simpson -- Principal Investigator ([email protected])  
 
 Use the help from the wiki below to setup a fork and personal branch in GitHub to put your developments
 on and keep up to date with the master branch of SLIM. Once the changes are sufficiently advanced you
 can form a Pull Request on GitHub. Either from your fork on GitHub, or from the main ESCOMP GitHub page
 for SLIM (be sure to hit the "compare across forks" link at the top of the page when you first create
 the pull request).
 
-https://github.com/ESCOMP/SLIM/pulls
+https://github.com/ESCOMP/SimpleLand/pulls
 
 This allows you to show your proposed changes and start getting feedback on them (even if they aren't finished). 
 This also allows your changes to be planned for and slated for a time to come into SLIM master. In most 
@@ -23,7 +23,7 @@ additional testing and bring the changes to SLIM master.
 
 #### SLIM Wiki:
 
-https://github.com/ESCOMP/SLIM/wiki
+https://github.com/ESCOMP/SimpleLand/wiki
 
 #### Code of Conduct:
 

Externals.cfg

@@ -1,32 +1,89 @@
 [slm]
 local_path = .
 protocol = externals_only
-externals = Externals_SLIM.cfg
 required = True
 
 [cam]
-tag = cam_cesm2_1_rel_53
+tag = cam6_3_071
 protocol = git
 repo_url = https://github.com/ESCOMP/CAM
 local_path = components/cam
 externals = Externals_CAM.cfg
 required = True
 
-[cice]
-tag = cice5_cesm2_1_1_20190321
+[cice6]
+tag = cesm_cice6_2_0_22
 protocol = git
-repo_url = https://github.com/ESCOMP/CESM_CICE5
+repo_url = https://github.com/ESCOMP/CESM_CICE
 local_path = components/cice
+externals = Externals.cfg
+required = True
+
+[cice5]
+tag = cice5_20220204
+protocol = git
+repo_url = https://github.com/ESCOMP/CESM_CICE5
+local_path = components/cice5
+required = True
+
+[ccs_config]
+tag = ccs_config_cesm0.0.38
+protocol = git
+repo_url = https://github.com/ESMCI/ccs_config_cesm.git
+local_path = ccs_config
+required = True
+
+[cdeps]
+tag = cdeps0.12.65
+protocol = git
+repo_url = https://github.com/ESCOMP/CDEPS
+local_path = components/cdeps
+externals =  Externals_CDEPS.cfg
+required = True
+
+[cmeps]
+tag = cmeps0.13.71
+protocol = git
+repo_url = https://github.com/ESCOMP/CMEPS
+local_path = components/cmeps
+required = True
+
+[cpl7]
+tag = cpl7.0.14
+protocol = git
+repo_url = https://github.com/ESCOMP/CESM_CPL7andDataComps
+local_path = components/cpl7
+required = True
+
+[share]
+tag = share1.0.13
+protocol = git
+repo_url = https://github.com/ESCOMP/CESM_share
+local_path = share
+required = True
+
+[mct]
+tag = MCT_2.11.0
+protocol = git
+repo_url = https://github.com/MCSclimate/MCT
+local_path = libraries/mct
+required = True
+
+[parallelio]
+tag = pio2_5_7
+protocol = git
+repo_url = https://github.com/NCAR/ParallelIO
+local_path = libraries/parallelio
 required = True
 
 [cime]
 local_path = cime
 protocol = git
+#repo_url = https://github.com/ESMCI/cime
 repo_url = https://github.com/ekluzek/cime
-hash = 25ba7866ec4835b148aac9f83242d0bc6257da5e
-#branch = add_slim_comp
+#tag = cime6.0.71
+hash = 9bbadb3b173c57f00ff8666790a474951e28391d
 required = True
 
 [externals_description]
-schema_version = 1.0.0
-
+schema_version = 1.0.01

README

@@ -3,15 +3,45 @@ Important files in main directories:
 =============================================================================================
 
 Externals.cfg --------------- File for management of the main high level externals
-Externals_SLIM.cfg ---------- File for management of the SLIM specific externals (if any)
 
 =============================================================================================
-    QUICKSTART: using the CPL7 scripts:
+Important main subdirectories
+=============================================================================================
+
+src --------------- SLIM Source code.
+tools ------------- SLIM Offline tools to prepare input datasets and process output.
+cime_config ------- Configuration files of cime for compsets and SLIM settings
+manage_externals -- Script to manage the external source directories
+py_env_create ----- Script to setup the python environment for SLIM python tools using conda
+python ------------ Some python modules
+components -------- Other active sub-components needed for SLIM to run (CAM and CICE)
+libraries --------- CESM libraries: MCT (Model Coupling Toolkit) and PIO
+share ------------- CESM shared code
+
+cime/scripts --------------- cesm/cime driver scripts
+
+=============================================================================================
+ SLIM XML variables:
+=============================================================================================
+
+SLIM_SCENARIO: Scenario to use, usually set by the compset
+SLIM_START_TYPE: The start type to use, usually set by the RUN_TYPE
+
+=============================================================================================
+ SLIM important namelist items:
+=============================================================================================
+
+mml_surdat -- Dataset of surface characteristics to use (usually set by the compset/grid)
+finidat ----- Initial conditions to startup with
+hist_nhtfrq - History file frequency of output
+
+=============================================================================================
+ QUICKSTART: using the CPL7 scripts:
 =============================================================================================
 
          cd cime/scripts
          ./create_newcase            # get help on how to run create_newcase
-         ./create_newcase --case testI --res f19_g17 --compset I2000SlimRsGs --mach cheyenne
+         ./create_newcase --case testI --res f19_f19_mg17 --compset I2000SlimRsGs
                                      # create new "I" case for cheyenne_intel at 1.9x2.5_gx1v7 res
                                      # "I2000SlimRsGs" case is SLIM active, datm8, and inactive ice/ocn/glc/rof
          cd testI

README.md

@@ -2,7 +2,8 @@
 Simple Land Model for CESM
 
 
-For instructions on how to run SLIM on it's own or coupled to CESM on Cheyenne, see the Wiki.
+For instructions on how to run SLIM on it's own or coupled to CESM on Cheyenne, see the Wiki, and the README file at the top of the
+SLIM checkout.
 
 To cite, please use:
 

README.rst

@@ -1,3 +1,5 @@
 ================
 SimpleLandModel
 ================
+
+SLIM the Simple Land Interface Model coupled to CESM2

README.testing

@@ -2,6 +2,8 @@
 #
 # The test list "aux_slim" is run as a test suite with the "create_test" script under cime/scripts
 # as follows.
+# NOTE: There are also tests for prealpha, prebeta for use with CESM testing
+#       And slim_sci to run a few standard tests for SLIM science
 #
 # Tests on cheyenne
 
@@ -24,6 +26,4 @@ nohup ./create_test --compare <baseline_comp> --generate <baseline_generate> mac
 nohup ./create_test --compare <baseline_comp> --generate <baseline_generate> machine izumi -r cases \
 --xml-category aux_slim --xml-machine izumi --xml-compiler gnu &
 nohup ./create_test --compare <baseline_comp> --generate <baseline_generate> machine izumi -r cases \
---xml-category aux_slim --xml-machine izumi --xml-compiler pgi &
-nohup ./create_test --compare <baseline_comp> --generate <baseline_generate> machine izumi -r cases \
 --xml-category aux_slim --xml-machine izumi --xml-compiler intel &

cime_config/buildlib

@@ -3,77 +3,88 @@
 """
 build slim ibrary
 """
-import sys, os, time, filecmp, shutil, imp
+import sys, os, time, filecmp
 
 _CIMEROOT = os.environ.get("CIMEROOT")
 if _CIMEROOT is None:
     raise SystemExit("ERROR: must set CIMEROOT environment variable")
 
-_LIBDIR = os.path.join(_CIMEROOT, "scripts", "Tools")
+_LIBDIR = os.path.join(_CIMEROOT, "CIME", "Tools")
 sys.path.append(_LIBDIR)
 
 from standard_script_setup import *
 from CIME.buildlib import parse_input
+from CIME.build import get_standard_makefile_args
 from CIME.case import Case
 from CIME.utils import run_cmd, expect
 
 logger = logging.getLogger(__name__)
 
 ###############################################################################
 def _main_func():
-###############################################################################
+    ###############################################################################
 
     caseroot, libroot, bldroot = parse_input(sys.argv)
 
     with Case(caseroot) as case:
 
         casetools = case.get_value("CASETOOLS")
+        makefile = os.path.join(casetools, "Makefile")
         lnd_root = case.get_value("COMP_ROOT_DIR_LND")
         gmake_j = case.get_value("GMAKE_J")
         gmake = case.get_value("GMAKE")
-        mach = case.get_value("MACH")
+        gmake_opts = get_standard_makefile_args(case)
+        driver = case.get_value("COMP_INTERFACE").lower()
         nthrds = case.get_value("LND_NTHRDS")
 
-        if ( nthrds > 1 ):
-            expect(False, "LND_NTHRDS must be 1 as threading isn't implemented (see issue #14)" )
+        if nthrds > 1:
+            expect(
+                False,
+                "LND_NTHRDS must be 1 as threading isn't implemented (see issue #14)",
+            )
 
-        #-------------------------------------------------------
+        # -------------------------------------------------------
         # create Filepath file
         #-------------------------------------------------------
+        compname = case.get_value("COMP_LND")
         filepath_file = os.path.join(bldroot,"Filepath")
         if not os.path.isfile(filepath_file):
             caseroot = case.get_value("CASEROOT")
-            paths = [os.path.join(caseroot,"SourceMods","src.slim"), 
+            expect( (compname == "slim"), "Unexpected COMP_LND name: %s" % (compname))
+            paths = [os.path.join(caseroot,"SourceMods","src."+compname), 
+                     os.path.join(lnd_root,"src","cpl",driver),
                      os.path.join(lnd_root,"src","main"),
                      os.path.join(lnd_root,"src","init_interp"),
                      os.path.join(lnd_root,"src","utils"),
                      os.path.join(lnd_root,"src","cpl")]
+
             # Paths needed to build the current system, but won't be long term
-            paths.append( os.path.join(lnd_root,"src","biogeophys") )
-            paths.append( os.path.join(lnd_root,"src","biogeochem") )
-            paths.append( os.path.join(lnd_root,"src","soilbiogeochem") )
+            paths.append(os.path.join(lnd_root, "src", "biogeophys"))
+            paths.append(os.path.join(lnd_root, "src", "biogeochem"))
+            paths.append(os.path.join(lnd_root, "src", "soilbiogeochem"))
 
             with open(filepath_file, "w") as filepath:
                 filepath.write("\n".join(paths))
                 filepath.write("\n")
-            
-        #-------------------------------------------------------
+
+        # -------------------------------------------------------
         # create the library in libroot
-        #-------------------------------------------------------
+        # -------------------------------------------------------
 
-        complib = os.path.join(libroot,"liblnd.a")
+        complib = os.path.join(libroot, "liblnd.a")
         makefile = os.path.join(casetools, "Makefile")
-        macfile  = os.path.join(caseroot, "Macros.%s" % mach)
 
-        cmd = "%s complib -j %d MODEL=slim COMPLIB=%s -f %s MACFILE=%s " \
-               % (gmake, gmake_j, complib, makefile, macfile )
+        cmd = "{} complib -j {} COMP_NAME={} COMPLIB={} -f {} {}" \
+               .format(gmake, gmake_j, compname, complib, makefile, gmake_opts )
 
         rc, out, err = run_cmd(cmd)
-        logger.info("%s: \n\n output:\n %s \n\n err:\n\n%s\n"%(cmd,out,err))
+        logger.info("%s: \n\n output:\n %s \n\n err:\n\n%s\n" % (cmd, out, err))
         expect(rc == 0, "Command %s failed with rc=%s" % (cmd, rc))
 
+
 ###############################################################################
 
 if __name__ == "__main__":
+    logger.warning( "WARNING: buildlib is being called as a program rather than a subroutine as " +
+                    "it is expected to be in the CESM context" )
     _main_func()
-

cime_config/buildnml

@@ -5,7 +5,9 @@ SLIM namelist creator executable
 """
 import sys, os
 
-_SLIM_PYTHON = os.path.normpath( os.path.join(os.path.dirname(os.path.abspath(__file__)), os.pardir, 'python') )
+_SLIM_PYTHON = os.path.normpath(
+    os.path.join(os.path.dirname(os.path.abspath(__file__)), os.pardir, "python")
+)
 sys.path.insert(1, _SLIM_PYTHON)
 
 from slim import add_cime_to_path
@@ -22,9 +24,12 @@ def _main_func():
 
     caseroot = parse_input(sys.argv)
     level = logging.WARNING
-    setup_logging( level )
+    setup_logging(level)
     with Case(caseroot) as case:
-        buildnml(case, caseroot, "slim")
+        compname = case.get_value("COMP_LND")
+        logger.warning( "WARNING: buildnml is being called as program rather than a subroutine " +
+                        "as it is expected to be in the CESM context" )
+        buildnml(case, caseroot, compname)
 
 
 if __name__ == "__main__":

cime_config/config_component.xml

@@ -29,7 +29,7 @@
   <entry id="SLIM_SCENARIO">
     <type>char</type>
     <default_value>global_uniform</default_value>
-    <valid_values>global_uniform,realistic_from_1850,realistic_from_2000</valid_values>
+    <valid_values>global_uniform,realistic_from_1850,realistic_from_2000,user_defined</valid_values>
     <values>
       <value compset="2000.*"   >realistic_from_2000</value>
       <value compset="1850.*_"  >realistic_from_1850</value>
@@ -40,6 +40,10 @@
     <desc>SLIM namelist use_case scenario.
       Determines the use-case scenario that will be used in the SLIM buildnml utility.
       This is normally set by the component set.
+        'global_uniform' is for surface conditions are globally constant
+        'realistic_from_1850' are surface conditions taken from a 1850 control simulation with CTSM
+        'realistic_from_2000' are surface conditions taken from a 2000 control simulation with CTSM
+        'user_defined' means the user will provide their own surface condition file (mml_surdat)
     </desc>
   </entry>